PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1SQ7
Asym. Unit
Info
Asym.Unit (82 KB)
Biol.Unit 1 (77 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
UNDERSTANDING PROTEIN LIDS: STRUCTURAL ANALYSIS OF ACTIVE HINGE MUTANTS IN TRIOSEPHOSPHATE ISOMERASE
Authors
:
I. Kursula, M. Salin, J. Sun, B. V. Norledge, A. M. Haapalainen, N. S. Sam R. K. Wierenga
Date
:
18 Mar 04 (Deposition) - 24 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Archae, Evolution, Flexible Loop-6, Tim, N-Hinge, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Kursula, M. Salin, J. Sun, B. V. Norledge, A. M. Haapalainen, N. S. Sampson, R. K. Wierenga
Understanding Protein Lids: Structural Analysis Of Active Hinge Mutants In Triosephosphate Isomerase
Protein Eng. Des. Sel. V. 17 375 2004
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TIM_2 (A:5-246,B:5-246)
2: TIM_1 (A:163-173,B:163-173)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TIM_2
PS51440
Triosephosphate isomerase (TIM) family profile.
TPIS_CHICK
5-246
2
A:5-246
B:5-246
2
TIM_1
PS00171
Triosephosphate isomerase active site.
TPIS_CHICK
163-173
2
A:163-173
B:163-173
[
close PROSITE info
]
Exons
(7, 14)
Info
All Exons
Exon 1.1 (A:2-38 | B:2-38)
Exon 1.2 (A:38-79 | B:38-79)
Exon 1.3 (A:79-107 | B:79-107)
Exon 1.4 (A:108-152 | B:108-152)
Exon 1.5 (A:152-180 | B:152-180)
Exon 1.6 (A:181-210 | B:181-210)
Exon 1.7 (A:210-248 | B:210-248)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSGALT00000023442
1
ENSGALE00000242044
chr1:
80431223-80431451
229
TPIS_CHICK
1-38
38
2
A:2-38
B:2-38
37
37
1.2
ENSGALT00000023442
2
ENSGALE00000153292
chr1:
80432287-80432410
124
TPIS_CHICK
38-79
42
2
A:38-79
B:38-79
42
42
1.3
ENSGALT00000023442
3
ENSGALE00000153290
chr1:
80432505-80432589
85
TPIS_CHICK
79-107
29
2
A:79-107
B:79-107
29
29
1.4
ENSGALT00000023442
4
ENSGALE00000153291
chr1:
80432725-80432857
133
TPIS_CHICK
108-152
45
2
A:108-152
B:108-152
45
45
1.5
ENSGALT00000023442
5
ENSGALE00000153294
chr1:
80433088-80433173
86
TPIS_CHICK
152-180
29
2
A:152-180
B:152-180
29
29
1.6
ENSGALT00000023442
6
ENSGALE00000153293
chr1:
80433324-80433411
88
TPIS_CHICK
181-210
30
2
A:181-210
B:181-210
30
30
1.7
ENSGALT00000023442
7
ENSGALE00000153295
chr1:
80433666-80434223
558
TPIS_CHICK
210-248
39
2
A:210-248
B:210-248
39
39
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1sq7a_ (A:)
1b: SCOP_d1sq7b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Triosephosphate isomerase (TIM)
(148)
Family
:
Triosephosphate isomerase (TIM)
(128)
Protein domain
:
Triosephosphate isomerase
(126)
Chicken (Gallus gallus) [TaxId: 9031]
(16)
1a
d1sq7a_
A:
1b
d1sq7b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1sq7A00 (A:2-248)
1b: CATH_1sq7B00 (B:2-248)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Chicken (Gallus gallus)
(18)
1a
1sq7A00
A:2-248
1b
1sq7B00
B:2-248
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_TIM_1sq7B01 (B:6-244)
1b: PFAM_TIM_1sq7B02 (B:6-244)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
TIM
(80)
Gallus gallus (Chicken)
(12)
1a
TIM-1sq7B01
B:6-244
1b
TIM-1sq7B02
B:6-244
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (82 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1SQ7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
